phenopackets phenopacket-reference-implementation issues

phenopackets / phenopacket-reference-implementation

Reference java implementation for phenopackets

BSD 3-Clause "New" or "Revised" License

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issues

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Add genotype to phenopacket

#84 pnrobinson opened 7 years ago
1
JsonGenerator.render java.lang.NoSuchMethodError

#83 pnrobinson opened 7 years ago
1
disease.setId

#82 pnrobinson closed 7 years ago
1
Remove requirements for lists in setters

#81 julesjacobsen opened 7 years ago
0
Consider using Immutables library

#80 julesjacobsen opened 7 years ago
1
disease should be a subclass of condition

#79 cmungall opened 8 years ago
0
Organism, Person -> Individual

#78 cmungall opened 8 years ago
0
Create carcinoma biosample example

#77 cmungall opened 8 years ago
0
Added contributor and date fields to associations.

#76 balhoff closed 8 years ago
0
Two more places to update new builder constructor.

#75 balhoff closed 8 years ago
0
Refactor pom to add plugin management and release profile

#74 heuermh opened 8 years ago
0
Updated code example in README.

#73 balhoff closed 8 years ago
0
Add static builder methods, including copy constructor

#72 heuermh closed 8 years ago
2
GPG artifact code signing should only be enabled in a release profile

#71 heuermh opened 8 years ago
1
Move RDF to Rdf to be consistent with Json and Yaml

#70 heuermh closed 8 years ago
2
Add metadata for associations

#69 cmungall opened 8 years ago
4
Added several non-empty list include annotations.

#68 balhoff closed 8 years ago
0
Fixed missing entity field values in RDF reader.

#67 balhoff closed 8 years ago
0
Add RO mappings into jsonld context file

#66 cmungall opened 8 years ago
0
Added handling of integer values to RDF reader.

#65 balhoff closed 8 years ago
0
Reading of PhenoPacket out of RDF.

#64 balhoff closed 8 years ago
0
Changed type of frequency from ConditionSeverity to ConditionFrequency.

#63 balhoff closed 8 years ago
0
Generate RDF with default context

#62 balhoff closed 8 years ago
0
added equals, hashCode and toString for Variant

#61 jnguyenx closed 8 years ago
0
Added reading of JSON-LD context, utility methods, and RDF output.

#60 balhoff closed 8 years ago
3
Fix for issue #42 and a few extra unit tests

#59 julesjacobsen closed 8 years ago
0
Make an AbstractEntity base class for all Entities

#58 julesjacobsen opened 8 years ago
3
first pass at exposures

#57 cmungall closed 8 years ago
0
Entity vs. ClassInstance

#56 selewis opened 8 years ago
1
Corrected typo 'variat_profile' -> 'variant_profile' and added requir…

#55 julesjacobsen closed 8 years ago
0
Added annotation for correct serialization of disease_occurrence key.

#54 balhoff closed 8 years ago
1
Add developer docs describing design pattern

#53 cmungall opened 8 years ago
0
Added variant association to the PhenoPacket builder

#52 tudorgroza closed 8 years ago
0
Added variant info according to the MME schema.

#51 tudorgroza closed 8 years ago
1
Failing test of JSON roundtrip (now with fix)

#50 balhoff closed 8 years ago
2
Jackson annotations for not writing empty lists

#49 balhoff closed 8 years ago
0
Updates for local snapshot usage.

#48 balhoff closed 8 years ago
0
Fixed warnings caused by missing generics.

#47 balhoff closed 8 years ago
0
Added methods for reading from input stream.

#46 balhoff closed 8 years ago
0
Added variant association to the Person builder model.

#45 tudorgroza closed 8 years ago
0
Consider adding a ClassInstance accessor for inferred_types

#44 cmungall opened 8 years ago
2
JsonGenerator doesn't seem to use jackson annotations

#43 cmungall closed 8 years ago
1
Correct example on the README

#42 cmungall closed 8 years ago
2
First pass at frequency/penetrance

#41 cmungall closed 8 years ago
0
Can null references be replaced with empty lists/strings and still not be written out?

#40 julesjacobsen opened 8 years ago
6
Fully operational README and a convenience method.

#39 julesjacobsen closed 8 years ago
1
OntologyClass - should encapsulate frequency?

#38 julesjacobsen closed 8 years ago
3
Swizzed-up the README.

#37 julesjacobsen closed 8 years ago
0
Fixing SO SF IRI

#36 cmungall closed 8 years ago
0
DO NOT MERGE YET: Measurement / quantitative phenotype support

#35 cmungall closed 8 years ago
0